rs1319956

Positions:

• chr14-19879052-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001005501.2(OR4K2):​c.*1840A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.345 in 148,904 control chromosomes in the GnomAD database, including 5,117 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.34 (5117 hom., cov: 40)
  • Exomes 𝑓: 0.38 (0 hom.)
• Consequence: OR4K2 NM_001005501.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.89

Genes affected

OR4K2 (HGNC:14728): (olfactory receptor family 4 subfamily K member 2) Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.598 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR4K2	NM_001005501.2	c.*1840A>G		3_prime_UTR_variant	2/2	ENST00000641885.1	NP_001005501.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR4K2	ENST00000641885.1	c.*1840A>G		3_prime_UTR_variant	2/2		NM_001005501.2	ENSP00000493007	P1
OR4K2	ENST00000641522.1	n.1244A>G		non_coding_transcript_exon_variant	3/3
OR4K2	ENST00000641785.1	n.1244A>G		non_coding_transcript_exon_variant	3/4

Frequencies

GnomAD3 genomes AF: 0.345 AC: 51278 AN: 148764 Hom.: 5096 Cov.: 40

Gnomad AFR AF: 0.393

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.615

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.334

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.361

GnomAD4 exome AF: 0.375 AC: 9 AN: 24 Hom.: 0 Cov.: 0 AF XY: 0.375 AC XY: 9 AN XY: 24

Gnomad4 ASJ exome AF: 0.250

Gnomad4 NFE exome AF: 0.389

GnomAD4 genome AF: 0.345 AC: 51343 AN: 148880 Hom.: 5117 Cov.: 40 AF XY: 0.348 AC XY: 25345 AN XY: 72766

Gnomad4 AFR AF: 0.393

Gnomad4 AMR AF: 0.438

Gnomad4 ASJ AF: 0.287

Gnomad4 EAS AF: 0.616

Gnomad4 SAS AF: 0.375

Gnomad4 FIN AF: 0.275

Gnomad4 NFE AF: 0.284

Gnomad4 OTH AF: 0.361

Alfa AF: 0.317 Hom.: 430

Asia WGS AF: 0.482 AC: 1675 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	13
DANN	Benign	0.78

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1319956; hg19: chr14-20347211;